data_5C4L # _model_server_result.job_id tBZkxdMAHo4TAlt1KkoKSg _model_server_result.datetime_utc '2024-12-01 11:14:46' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5c4l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 5C4L # _exptl.entry_id 5C4L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 447.526 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.18 _cell.angle_gamma 90 _cell.entry_id 5C4L _cell.length_a 74.22 _cell.length_b 65.04 _cell.length_c 78.78 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C4L _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C19 H37 N5 O7' _chem_comp.formula_weight 447.526 _chem_comp.id SIS _chem_comp.mon_nstd_flag . _chem_comp.name '(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Sisomicin # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O43 C43 SIS sing 312 n n C83 C43 SIS sing 313 n n C43 C53 SIS sing 314 n n C43 C33 SIS sing 315 n n N33 C33 SIS sing 316 n n N33 C93 SIS sing 317 n n C53 O53 SIS sing 318 n n C33 C23 SIS sing 319 n n O53 C13 SIS sing 320 n n C23 C13 SIS sing 321 n n C23 O23 SIS sing 322 n n C13 O62 SIS sing 323 n n O62 C62 SIS sing 324 n n O52 C52 SIS sing 325 n n C62 C52 SIS sing 326 n n C62 C12 SIS sing 327 n n N12 C12 SIS sing 328 n n C52 C42 SIS sing 329 n n C12 C22 SIS sing 330 n n C42 O11 SIS sing 331 n n C42 C32 SIS sing 332 n n C22 C32 SIS sing 333 n n C11 O11 SIS sing 334 n n C11 O51 SIS sing 335 n n C11 C21 SIS sing 336 n n N21 C21 SIS sing 337 n n O51 C51 SIS sing 338 n n C32 N32 SIS sing 339 n n C21 C31 SIS sing 340 n n C51 C61 SIS sing 341 n n C51 C41 SIS doub 342 n n N61 C61 SIS sing 343 n n C31 C41 SIS sing 344 n n C11 H1 SIS sing 345 n n C12 H2 SIS sing 346 n n C13 H3 SIS sing 347 n n C21 H4 SIS sing 348 n n C22 H5 SIS sing 349 n n C22 H6 SIS sing 350 n n C23 H7 SIS sing 351 n n C31 H8 SIS sing 352 n n C31 H9 SIS sing 353 n n C32 H10 SIS sing 354 n n C33 H11 SIS sing 355 n n C41 H12 SIS sing 356 n n C42 H13 SIS sing 357 n n C52 H14 SIS sing 358 n n C53 H15 SIS sing 359 n n C53 H16 SIS sing 360 n n C61 H17 SIS sing 361 n n C61 H18 SIS sing 362 n n C62 H19 SIS sing 363 n n C83 H20 SIS sing 364 n n C83 H21 SIS sing 365 n n C83 H22 SIS sing 366 n n C93 H23 SIS sing 367 n n C93 H24 SIS sing 368 n n C93 H25 SIS sing 369 n n N12 H26 SIS sing 370 n n N12 H27 SIS sing 371 n n N21 H29 SIS sing 372 n n N21 H30 SIS sing 373 n n N32 H32 SIS sing 374 n n N32 H33 SIS sing 375 n n N33 H35 SIS sing 376 n n N61 H37 SIS sing 377 n n N61 H38 SIS sing 378 n n O23 H40 SIS sing 379 n n O43 H41 SIS sing 380 n n O52 H42 SIS sing 381 n n # _atom_sites.entry_id 5C4L _atom_sites.fract_transf_matrix[1][1] 0.013473 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000278 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015375 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012696 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 4XR A 1 401 2 4XR SIT . D 3 SIS B 1 401 1 SIS SIS . E 4 HOH A 1 501 35 HOH HOH . E 4 HOH A 2 502 48 HOH HOH . E 4 HOH A 3 503 28 HOH HOH . E 4 HOH A 4 504 10 HOH HOH . E 4 HOH A 5 505 42 HOH HOH . E 4 HOH A 6 506 13 HOH HOH . E 4 HOH A 7 507 40 HOH HOH . E 4 HOH A 8 508 36 HOH HOH . E 4 HOH A 9 509 43 HOH HOH . E 4 HOH A 10 510 5 HOH HOH . E 4 HOH A 11 511 33 HOH HOH . E 4 HOH A 12 512 31 HOH HOH . E 4 HOH A 13 513 30 HOH HOH . E 4 HOH A 14 514 9 HOH HOH . E 4 HOH A 15 515 1 HOH HOH . E 4 HOH A 16 516 55 HOH HOH . E 4 HOH A 17 517 49 HOH HOH . E 4 HOH A 18 518 16 HOH HOH . E 4 HOH A 19 519 18 HOH HOH . E 4 HOH A 20 520 41 HOH HOH . E 4 HOH A 21 521 39 HOH HOH . E 4 HOH A 22 522 32 HOH HOH . E 4 HOH A 23 523 14 HOH HOH . E 4 HOH A 24 524 11 HOH HOH . E 4 HOH A 25 525 15 HOH HOH . E 4 HOH A 26 526 54 HOH HOH . E 4 HOH A 27 527 8 HOH HOH . E 4 HOH A 28 528 7 HOH HOH . E 4 HOH A 29 529 29 HOH HOH . E 4 HOH A 30 530 17 HOH HOH . E 4 HOH A 31 531 44 HOH HOH . E 4 HOH A 32 532 6 HOH HOH . F 4 HOH B 1 501 38 HOH HOH . F 4 HOH B 2 502 23 HOH HOH . F 4 HOH B 3 503 24 HOH HOH . F 4 HOH B 4 504 19 HOH HOH . F 4 HOH B 5 505 46 HOH HOH . F 4 HOH B 6 506 21 HOH HOH . F 4 HOH B 7 507 26 HOH HOH . F 4 HOH B 8 508 4 HOH HOH . F 4 HOH B 9 509 45 HOH HOH . F 4 HOH B 10 510 34 HOH HOH . F 4 HOH B 11 511 50 HOH HOH . F 4 HOH B 12 512 25 HOH HOH . F 4 HOH B 13 513 47 HOH HOH . F 4 HOH B 14 514 20 HOH HOH . F 4 HOH B 15 515 53 HOH HOH . F 4 HOH B 16 516 27 HOH HOH . F 4 HOH B 17 517 37 HOH HOH . F 4 HOH B 18 518 51 HOH HOH . F 4 HOH B 19 519 22 HOH HOH . F 4 HOH B 20 520 3 HOH HOH . F 4 HOH B 21 521 52 HOH HOH . F 4 HOH B 22 522 2 HOH HOH . F 4 HOH B 23 523 12 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C11 SIS . . . D 3 0.86 -9.387 108.676 1 62.51 ? C11 SIS 401 B 1 HETATM 2 C C12 SIS . . . D 3 0.957 -5.732 112.671 1 68.99 ? C12 SIS 401 B 1 HETATM 3 C C13 SIS . . . D 3 -2.447 -4.961 112.05 1 68.23 ? C13 SIS 401 B 1 HETATM 4 C C21 SIS . . . D 3 1.238 -10.858 108.314 1 66.26 ? C21 SIS 401 B 1 HETATM 5 C C22 SIS . . . D 3 2.204 -5.836 111.825 1 61.2 ? C22 SIS 401 B 1 HETATM 6 C C23 SIS . . . D 3 -3.11 -4.206 113.213 1 68.82 ? C23 SIS 401 B 1 HETATM 7 C C31 SIS . . . D 3 1.386 -11.096 106.825 1 65.34 ? C31 SIS 401 B 1 HETATM 8 C C32 SIS . . . D 3 2.351 -7.302 111.314 1 66.77 ? C32 SIS 401 B 1 HETATM 9 C C33 SIS . . . D 3 -3.87 -5.151 114.185 1 69.78 ? C33 SIS 401 B 1 HETATM 10 C C41 SIS . . . D 3 1.056 -9.983 106.024 1 60.07 ? C41 SIS 401 B 1 HETATM 11 C C42 SIS . . . D 3 1.153 -7.685 110.398 1 63.26 ? C42 SIS 401 B 1 HETATM 12 C C43 SIS . . . D 3 -4.764 -6.207 113.389 1 73.31 ? C43 SIS 401 B 1 HETATM 13 C C51 SIS . . . D 3 1.154 -8.697 106.557 1 64.69 ? C51 SIS 401 B 1 HETATM 14 C C52 SIS . . . D 3 -0.209 -7.416 111.14 1 69.3 ? C52 SIS 401 B 1 HETATM 15 C C53 SIS . . . D 3 -3.946 -6.846 112.24 1 66.01 ? C53 SIS 401 B 1 HETATM 16 C C61 SIS . . . D 3 0.967 -7.565 105.807 1 59.31 ? C61 SIS 401 B 1 HETATM 17 C C62 SIS . . . D 3 -0.265 -5.972 111.77 1 69.76 ? C62 SIS 401 B 1 HETATM 18 C C83 SIS . . . D 3 -5.195 -7.357 114.326 1 71.37 ? C83 SIS 401 B 1 HETATM 19 C C93 SIS . . . D 3 -4.462 -4.849 116.534 1 69.82 ? C93 SIS 401 B 1 HETATM 20 N N12 SIS . . . D 3 0.873 -4.46 113.422 1 67.78 ? N12 SIS 401 B 1 HETATM 21 N N21 SIS . . . D 3 2.467 -11.326 109.03 1 63.6 ? N21 SIS 401 B 1 HETATM 22 N N32 SIS . . . D 3 3.641 -7.511 110.613 1 67.38 ? N32 SIS 401 B 1 HETATM 23 N N33 SIS . . . D 3 -4.67 -4.37 115.166 1 68.51 ? N33 SIS 401 B 1 HETATM 24 N N61 SIS . . . D 3 2.355 -7.061 105.57 1 64.57 ? N61 SIS 401 B 1 HETATM 25 O O11 SIS . . . D 3 1.248 -9.077 110.018 1 60.93 ? O11 SIS 401 B 1 HETATM 26 O O23 SIS . . . D 3 -2.083 -3.533 113.95 1 80.91 ? O23 SIS 401 B 1 HETATM 27 O O43 SIS . . . D 3 -5.976 -5.589 112.794 1 70.67 ? O43 SIS 401 B 1 HETATM 28 O O51 SIS . . . D 3 1.55 -8.495 107.859 1 62.1 ? O51 SIS 401 B 1 HETATM 29 O O52 SIS . . . D 3 -1.381 -8.168 110.46 1 66.07 ? O52 SIS 401 B 1 HETATM 30 O O53 SIS . . . D 3 -3.356 -5.846 111.397 1 70.8 ? O53 SIS 401 B 1 HETATM 31 O O62 SIS . . . D 3 -1.431 -5.83 112.563 1 71.89 ? O62 SIS 401 B 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #